Genomes are generally viewed as static, at least throughout the life cycle of any particular species. Yet evidence from lineages across the eukaryotic tree of life indicates that genomes can be dynamic. Evidence of genome dynamics includes varying levels of DNA (i.e. ploidy levels), amplification of specific regions of the genome, and chromosomal rearrangements analogous to those found in human immune cells. These data suggest that eukaryotes may have the ability to distinguish between the DNA that they will pass on to future generations from other genetic material that is more malleable. In some lineages, like animals, there is a physical separation between germline and somatic genomes. In other eukaryotes, it is possible that epigenetic marks such as chromatin modification play a role in distinguishing germline from somatic material. The proposed work will test three interrelated hypotheses on the nature of eukaryotic genomes by 1) reconstructing the evolutionary history of genes involved in marking genomes; 2) elucidating specific mechanisms used to distinguish germline and somatic genomes in the ciliate C. uncinata; and 3) collecting next generation sequence data from a variety of ciliates to enable comparative analyses in this ~1 billion year old clade. Data will be collected using a modified phylogenomic pipeline and high throughput sequencing of both populations and single cells. Hypotheses will be analyzed using both bioinformatics and population genetic tools (e.g. maximum likelihood analyses of gene gains/losses and patterns of substitutions). The proposed work will take place at Smith College, an all women's predominantly undergraduate institution. Each year, undergraduates will participate directly in the research and learn about the results in one of the courses taught by the PI. This project will also enable training of a graduate student participating through the Organismic and Evolutionary Biology Program at UMass-Amherst. 1